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MChem Chemistry with Medicinal Chemistry

Year of entry: 2024

Course unit details:
Structure and reactivity of organic molecules

Course unit fact file
Unit code CHEM20412
Credit rating 10
Unit level Level 2
Teaching period(s) Semester 2
Offered by Department of Chemistry
Available as a free choice unit? No


This course unit detail provides the framework for delivery in 21/22 and may be subject to change due to any additional Covid-19 impact.  Please see Blackboard / course unit related emails for any further updates

Weeks 1-4: Rings and Stereoelectronics (Dr Nathan Owston)

Weeks 5-8: Introduction to Primary Metabolites 

Weeks 9-12: Retrosynthetic Analysis (Dr Andrew Regan)



Unit title Unit code Requirement type Description
Introductory Chemistry CHEM10101 Pre-Requisite Compulsory
Energy and Change CHEM10212 Pre-Requisite Compulsory
Coordination Chemistry CHEM10312 Pre-Requisite Compulsory
Structure and Reactivity CHEM10412 Pre-Requisite Compulsory
Organic Synthesis CHEM20411 Pre-Requisite Compulsory


To extend the concepts presented in previous courses to the structural, mechanistic, physical and biological properties of organic molecules.

Learning outcomes

On successful completion of the course students should be able to:

  • Apply knowledge of structure and bonding to the kinetics associated with bond rotation and interconversion, and rationalise their consequences for spectroscopy and mechanism.
  • Predict whether organic reactions will occur through consideration of stereoelectronic effects, basic kinetics and thermodynamics.
  •  Evaluate and propose strategies for the synthesis of cyclic molecules based on consideration of stereoelectronic effects, basic kinetics and thermodynamics.
  • Apply the concepts of reactivity, stereochemistry and stereoelectronics to evaluate the nature of carbohydrates.
  • Use knowledge of the nature of carbohydrates and protecting group strategies to evaluate the outcomes of reactions and construct synthetic routes to oligosaccharides.
  • Apply the concepts of reactivity, stereochemistry and stereoelectronics to evaluate the nature of amino acids and select methods appropriate for their synthesis.
  • Use knowledge of the nature of amino acids, protecting group strategies and solid phase synthesis to generate synthetic strategies for the synthesis of oligopeptides.
  • Use knowledge of oligopepetide analysis, for sequencing and composition, to evaluate the primary (and secondary) structure of oligopeptides.
  • Choose appropriate disconnections for difunctional target molecules, based on stabilities of the synthons generated
  • Analyse the relationships between functional groups in difunctional compounds
  • Choose appropriate synthetic equivalents for synthons resulting from retrosynthetic analysis
  • Choose appropriate reagents for the reactions involved in planned syntheses
  • Decide whether any extra methods of control are required for a synthesis to proceed as planned


Transferable skills and personal qualities

  • Problem-solving skills: Manipulation of chemical structures and using multiple models, e.g. 2D into 3D and vice versa. Determination of reaction mechanisms and rationalizing reaction selectivity by consideration of steric and electronic factors. Evaluating synthetic routes and choosing and proposing syntheses and retrosyntheses using a logical, analytical approach.
  • Numeracy and mathematical skills:(e.g.determination of mole fraction from polarimetry & graphical information)
  • Analytical skills (e.g. spectroscopy and link to mechanism, analysis of chromatographic evidence for peptide composition)
  • Communications skills (written and oral communication using chemical terminology and technical vocabulary)


Assessment methods

Method Weight
Written exam 100%

Feedback methods

CHEM20412 is delivered in a way which allows students to regularly receive feedback on their work and progress in lecture time. This is achieved through a significant amount of content being delivered as worked examples/content/problems during lectures. Such delivery allows provision of formative feedback through material, comments and suggestions which are designed to help guide students in their own conceptualization and approach to solving problems.

Worked content and problems offer opportunities for both facilitator and peer feedback by

  • Providing opportunities for students to master concepts introduced in lectures, and apply these concepts to unseen material.
  • Encouraging development of thinking skills (with a focus on critical thinking, analysis, evaluation and application, rather than simple reproduction of knowledge/process)
  • Promoting teamwork and collaboration, and the development of skills associated with this, as well as individual responsibility for learning.
  • Providing time for students to reflect upon their own learning, and to self-evaluate.

In addition, facilitators share problem-solving approaches/common misconceptions through whole-class feedback.


In addition to the above, three tutorials provide opportunities for more personalised tutor feedback and for informal peer feedback on CHEM20412 material in a collaborative, small-group environment.


CHEM20412 is supported by a selection of supplementary E-learning materials which provide an opportunity for students to evaluate their own progress during the module.

Exam technique and revision sessions

Provide an opportunity to deliver assessment-specific feedback relating to assessment criteria and understanding of question demand, as well as concerning problem solving in examinations (using past paper questions as exemplars).


Individual lecturers provide office hours or operate an open-door policy to provide individual, personalised feedback.


Recommended reading

• J. Clayden, N. Greeves, and S. Warren, Organic Chemistry, 2nd edition (Oxford University Press, 2012), ISBN 978-0199270-29-3.

• S. Doonan, Peptides and Proteins, RSC Tutorial Chemistry Texts (RSC, Cambridge, 2002), ISBN 0-85404-692-5

• S. Warren, Organic Synthesis: the Disconnection Approach, Wiley, 2nd edition, 2008; classmark 545.9/W55). The first edition is also useful: (1982); classmark 545.9/W8. Workbook at 545.9/W5 (also available as an online e-book).

• S. Warren, Designing organic syntheses : a programmed introduction to the synthon approach, Wiley, (1978) (classmark: 545.9/W9) (9 copies)


The following Oxford University Press Chemistry Primers are recommended, and are freely available to students as e-books via the University Library catalogue and Bibliotech:

  • A. J. Kirby, Stereoelectronic Effects, 1996.
  • B. G. Davis & A. G. Fairbanks, Carbohydrate Chemistry, 2002.
  • C. M. Dobson, J. A. Gerrard & A. J. Pratt, Foundations of Chemical Biology, 2001
  • J. Jones, Amino Acid & Peptide Synthesis, 2002.
  • C. L. Willis and M. Wills, Organic Synthesis, 1991.
  • R. S. Ward, Bifunctional Compounds, 1994.
  • J. Jones, Core Carbonyl Chemistry 1997.

A set of molecular models is also highly recommended.


Study hours

Scheduled activity hours
Assessment written exam 2
Lectures 24
Tutorials 3
Independent study hours
Independent study 71

Teaching staff

Staff member Role
Andrew Regan Unit coordinator
Neil Dixon Unit coordinator
Nathan Owston Unit coordinator

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